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- EMDB-20122: non-decorated head of the phage T5 -

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Basic information

Entry
Database: EMDB / ID: EMD-20122
Titlenon-decorated head of the phage T5
Map data
SampleEscherichia phage T5 (bacteriophage):
virus / Major capsid protein
Function / homologyPhage capsid / Phage capsid family / viral scaffold / T=13 icosahedral viral capsid / viral capsid / Major capsid protein
Function and homology information
Biological speciesEscherichia phage T5 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsHuet A / Duda RL / Boulanger P / Conway JF
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteR01 GM047795 United States
National Institutes of Health/National Human Genome Research InstituteS10 OD019995 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Capsid expansion of bacteriophage T5 revealed by high resolution cryoelectron microscopy.
Authors: Alexis Huet / Robert L Duda / Pascale Boulanger / James F Conway /
Abstract: The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a ...The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a regulated process that involves several intermediates, including a thick-walled round precursor prohead that expands as the viral DNA is packaged to yield a thin-walled and angular mature capsid. We investigated capsid maturation by comparing cryoelectron microscopy (cryo-EM) structures of the prohead, the empty expanded capsid both with and without decoration protein, and the virion capsid at a resolution of 3.8 Å for the latter. We detail the molecular structure of the mcp, its complex pattern of interactions, and their evolution during maturation. The bacteriophage T5 mcp is a variant of the canonical HK97-fold with a high level of plasticity that allows for the precise assembly of a giant macromolecule and the adaptability needed to interact with other proteins and the packaged DNA.
Validation ReportPDB-ID: 6oma

SummaryFull reportAbout validation report
History
DepositionApr 18, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseOct 2, 2019-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 11
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 11
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6oma
  • Surface level: 11
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6oma
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20122.map.gz / Format: CCP4 / Size: 474 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.11 Å/pix.
x 499 pix.
= 1052.89 Å
2.11 Å/pix.
x 499 pix.
= 1052.89 Å
2.11 Å/pix.
x 499 pix.
= 1052.89 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.11 Å
Density
Contour LevelBy AUTHOR: 11.0 / Movie #1: 11
Minimum - Maximum-6.7652707 - 22.827423
Average (Standard dev.)0.0046043587 (±2.3287013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-249-249-249
Dimensions499499499
Spacing499499499
CellA=B=C: 1052.8899 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.112.112.11
M x/y/z499499499
origin x/y/z0.0000.0000.000
length x/y/z1052.8901052.8901052.890
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS-249-249-249
NC/NR/NS499499499
D min/max/mean-6.76522.8270.005

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Supplemental data

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Sample components

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Entire Escherichia phage T5

EntireName: Escherichia phage T5 (bacteriophage) / Number of components: 2

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Component #1: virus, Escherichia phage T5

VirusName: Escherichia phage T5 / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: OTHER
MassTheoretical: 26 MDa
SpeciesSpecies: Escherichia phage T5 (bacteriophage)
Source (natural)Host Species: Escherichia coli (E. coli)
Shell #1Name of element: ND-head / Diameter: 700.0 Å / T number (triangulation number): 13

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Component #2: protein, Major capsid protein

ProteinName: Major capsid protein / Number of Copies: 13 / Recombinant expression: No
MassTheoretical: 32.931359 kDa
SourceSpecies: Escherichia phage T5 (bacteriophage)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL / pH: 7.6
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: OTHER / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3628

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 21233
3D reconstructionSoftware: Auto3DEM / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 2FT1
Output model

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